I've used MatrixEQTL to find eQTLs and got the p-values. I ran these p-values through GenABEL to get inflation factor lambda. However, what to do next? Based on GWAS analysis, I should divide each Chi-square statistics with this factor, regenerate p-values, and calculate q-values, is it correct? However, for eQTLs, I only have t-stat, should I use t-stat to do the same thing (new_pval = pt ( -abs ( t-stat / lambda ), df ) * 2 ) ? Thanks a lot.
•
written
by
Zhenyu Zhang
1 answer
I think that the most correct thing is the following, I hope that someone can confirm (or contradict) this:
1) Transform all your pvalues in chi-square values with one df using qchisq function, and set lower.tail=FALSE
2) Run genabel to estimate lambda (you can estimate lambda based on chisquare values as well)
3) Divide the chisquare values by lambda
4) Compute the pvalues from the new chisquare values using the function pchisq, again setting lower.tail=F
Log in to answer this question.
-
Lambda GC, genomic inflation and REGENIE
written by Zhiyi •
-
Best software for hQTL analysis with the aim of performing MR analysis
written by chrisclarkson100
-
Dealing with P value inflation of SNPs identified by qqplot
written by stephen.johnson.online •
-
Adding Principal components as covariates in GWAS studies
written by anikcropscience •
-
How to find Standard Error (SE) values when not provided in GWAS summary stats?
written by ydadmehr •
-
Understanding and adjusting for genomic inflation factor in GWAS
written by f.abbondanza94 •
-
genomic inflation factor and how to use it to estimate adjusted P-values in GWAS?
written by Ana
-
converting very small p-values into chi-squared statistics with python
written by yorgos.athanasiadis •
-
Calculate genomic inflation factor lambda for meta-analysis run in PLINK?
written by dam4l
-
Computing Genome Inflation Factor Lambda
written by Brian Tsai •
